Body size represents a complex phenotype driven by genetic variation and epigenetic regulation, with the molecular processes underlying this trait remaining a central challenge to disentangle. To elucidate these fundamental mechanisms, we apply a multi-omics approach that combines ROH-based selection mapping with growth plate epigenomics in pigs. Taking advantage of divergent selection that separates pigs into miniature and larger-sized groups, we target genomic regions under this intense selection for height, which harbour functional variants with pronounced effects. We assemble a multi-omics dataset, identifying homozygous alternative SNPs in Aachen Minipigs and Mini-LEWE predicted to affect cis-regulatory elements potentially interacting with differentially expressed genes that drive body size in breed-dependent ways. Our results point to an lncRNA (ENSSSCG00000048200) near SDR16C5 and PLAG1, HPX and NET-related pathways, as central players in the growth plates. In summary, our study offers a multi-layered characterisation of regulatory mechanisms in the growth plates in the pig model.
